A Peek into the Plasmidome of Global Sewage – Philipp Kirstahler – mSystems *The authors describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes.
The social dilemmas of climate change and antibiotic resistance: an analytic comparison and discussion of policy implications – Niklas Harring – Humanities and Social Sciences Communications *This article analyses climate change and antimicrobial resistance within the context of game theory. Previous literature has identified these problems as common tragedies, where inherent incentive structures encourage selfish overuse of existing resources. While the game theoretical models provide a helpful conceptual basis, the present analysis suggests discrepancies between some of the theoretical assumptions and the practical realities of climate change and antimicrobial resistance.
Review: Antibiotic resistance: time of synthesis in a post-genomic age – Teresa Gil-Gil – Computational and Structural Biotechnology Journal *The authors analyzed the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
Mobile antimicrobial resistance genes in probiotics – Adrienn Gréta Tóth – bioRxiv *The authors raised clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.
Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil – Kimberley V. Sukhum – mBio *The authors evaluated that on dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, they collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons and used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms.
Dissipation of antibiotic resistance genes in manure-amended agricultural soil – Liang-Ying He – Science of The Total Environment *This study provides insight into the dissipation of antibiotic resistance genes in manure-applied agricultural soil. The continuous application of manure results in accumulation of ARGs which persists in soil for at least two years.
Environmental fate of tetracycline antibiotics: degradation pathway mechanisms, challenges, and perspectives – Ahmad Fiaz – Environmental Sciences Europe *The authors collected data on the available degradation strategies, mechanisms involved in biodegradable and non-biodegradable routes, the main factor affecting degradation strategies, compiled novel detection techniques of tetracycline antibiotics in the environment, and discussed antibiotic resistance genes and their potential role in degradation.
Water environment
Wastewater treatment plants as a reservoir of integrase and antibiotic resistance genes – An epidemiological threat to workers and environment – Wiktor Zieliński – Environmental International *The authors found a significant increase in the quantities of ARGs and concentrations of antibiotics in the river following the discharge of treated wastewater in comparison to their amounts in the river water upstream from the point of discharge. A higher concentration of ARGs was detected in the DNA from swabs obtained from the wastewater treatment plant employees than from ones collected from the control group.
Geographical specificity in public transit air resistome. Heatmap of the top 30 AR protein families based on average reads per kilobase per million (RPKM) reads across metagenomes. Core AR protein families (those detected in ≥ 75% of the entire dataset) are indicated in red and asterisks
Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies – Wen Shi Lee – Nature Microbiology *The authors described the key ADE mechanisms and discussed mitigation strategies for SARS-CoV-2 vaccines and therapies in development and about the risk of ADE in SARS-CoV-2. They outline recently published data to evaluate the risks and opportunities for antibody-based protection against SARS-CoV-2.
Our April AMR digest features recent studies on antibiotics resistance in gut microbiota, prediction and quick diagnosis models as well as the role of birds and sewage water in AMR dissemination.
Join the SPRING AMR WEBINARS to discuss the latest AMR insights with us and our invited speakers. You can register HERE for the next webinar on May 19 with Heike Schmitt and Etienne Ruppé.
Forecasting the dissemination of antibiotic resistance genes across bacterial genomes – Mostafa M. H. Ellabaan – Nature Communications *The authors predict the potential future dissemination of known ARGs by using statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes.
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation – Fabienne Antunes Ferreira – Microbial Genomics *This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. The suggested protocol includes: (1) a 20 h sequencing run; (2) identification of the sequence type (ST); (3) de novo genome assembly; (4) polishing of the draft genomes; and (5) phylogenetic analysis based on SNPs.
Review: Epidemiology and Molecular Basis of Multidrug Resistance in Rhodococcus equi – Sonsiray Álvarez Narváez – Microbiology and Molecular Biology Reviews *This review summarizes the factors that contributed to the development and spread of MDR R. equi, the molecular epidemiology of the emergence of MDR R. equi, the repercussions of MDR R. equi for veterinary and human medicine, and measures that might mitigate antimicrobial resistance at horse-breeding farms, such as alternative treatments to traditional antibiotics.
CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens – Elizabeth Pursey – BioRxiv *The authors modelled the association between CRISPR-Cas and indicators of horizontal gene transfer and found that pathogens with a CRISPR-Cas system were less likely to carry antibiotic resistance genes than those lacking this defence system.
Environmental microbiology
Review: Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges – Anh Q. Nguyen – Science of the Total Environment *Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. This review highlights significant knowledge gaps including inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment.
March digest features review on nonlytic antimicrobial functions of complement, metabolic fitness models, BActeriophage SElection for your Laboratory (a collection of representative E. coli phages), Dr Dirt game, and more. Check out our list of AMR focused podcasts. Enjoy!
And, we are exciting to share with you EMBARK NEWS – the SPRING AMR WEBINARS! Join us and our invited speakers to discuss the latest AMR insights. Register for the first webinar on April 28 with Gerry Wright and Luis Pedro CoelhoHERE.
Metabolic fitness landscapes predict the evolution of antibiotic resistance – Fernanda Pinheiro – Nature Ecology & Evolution *Pinheiro et al. developed a metabolic model of antibiotic resistance that predicts the dosage-response of common resistance mutants and prevalent resistance mechanisms depending on drug levels and nutrient conditions. These predictions are confirmed by empirical growth inhibition curves and genomic data of Escherichia coli populations exposed to streptomycin challenge.
Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Andrew D. Letten – The ISME Journal *Letten et al. found strong evidence of community-level suppression of the resistant strain in the absence of antibiotics and, despite large changes in community composition and abundance following rifampicin exposure, suppression of the invading resistant strain was maintained in both antibiotic treatments.
Vertical distribution of antibiotic resistance genes in an urban green facade – Shu-Yi-Dan Zhou – Environment International *Study suggests that microorganisms may move from soil to plant, potentially through an endophytic mechanism and thus, there is a clear potential for movement of ARGs and human pathogens from the outdoor environment.
Unraveling the riverine antibiotic resistome: the downstream fate of anthropogenic inputs – Jangwoo Lee – Water Research *Great work on drivers of riverine resistomes, pinpointing monitoring targets to identify where human sources and exposures are likely to be most acute. The authors observed the increase of certain gene markers downstream, without obvious sources of anthropogenic contamination.
Dr Dirt – a simulation game from Hoskisson Lab and Game Doctor team on antibiotic discovery
And the Microbes – a comic by Edward Ross and Jamie Hall: Join Luna and her sulky brother Simon on a journey into the weird and wonderful world of microbes.
February digest highlights the current state of vaccines against resistant bacterial pathogens and novel ways by which they can evolve resistance, effects of common sweeteners on conjugation rate and how international travel contributes to spread of multidrug-resistant bacteria, and much more. Check out our selection of AMR focused podcast episodes and webinars. Happy reading!
*Mutations targeting central carbon and energy metabolism arise in response to antibiotic treatment. These mutations confer resistance and are highly prevalent in clinical pathogens, expanding the known means by which pathogenic microbes can evolve resistance.
Tackling Antibiotic Resistance: What Should Dental Teams Do? – British Society for Antimicrobial Chemotherapy and FDI World Dental Federation Discover the danger posed by antibiotic resistance, and how dental teams can meet the challenge to protect patients.
*Mutations targeting central carbon and energy metabolism arise in response to antibiotic treatment. These mutations confer resistance and are highly prevalent in clinical pathogens, expanding the known means by which pathogenic microbes can evolve resistance.